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wiki:curtain_bin_vs_txt [2018/07/27 16:21]
david [old]
wiki:curtain_bin_vs_txt [2018/07/27 16:36] (current)
david [Some other binary types]
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 ==== Some other binary types ==== ==== Some other binary types ====
  
 +===== Executable =====
 <​code>​ <​code>​
 $ file /bin/ls $ file /bin/ls
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 You see that the command //ls// is actually a computer program that is a binary executable. ​ You see that the command //ls// is actually a computer program that is a binary executable. ​
  
 +===== Binary Alignment Map =====
 <​code>​ <​code>​
 $ file AR122.bam $ file AR122.bam
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 As with binary data, text data can have a more specific format. The extensions: //.txt, .sh, .bash, .c, .gff, fasta, .py// are all common file extensions that a genomics user sees on a linux computer. ​ As with binary data, text data can have a more specific format. The extensions: //.txt, .sh, .bash, .c, .gff, fasta, .py// are all common file extensions that a genomics user sees on a linux computer. ​
  
-It is up to the genomicistand the programs he or she usesto produce ​and/or validate files with the given formats.+It is up to the genomicist and the programs he or she uses to produce/​validate files with the given formats.
  
 Examples of text formats in genomics. Examples of text formats in genomics.
  
 ^ Filetype ^ description ^ extension ^ format definition ^ ^ Filetype ^ description ^ extension ^ format definition ^
-| Fasta | DNA/​RNA/​Protein sequence with header | .fasta, .fa | link | +| Fasta | DNA/​RNA/​Protein sequence with header | .fasta, .fa | [[http://​genetics.bwh.harvard.edu/​pph/​FASTA.html|link]] 
-| Fastq | DNA/​RNA/​Protein sequence with header + quality information | .fastq, .fq | link | +| Fastq | DNA/​RNA/​Protein sequence with header + quality information | .fastq, .fq | [[http://​maq.sourceforge.net/​fastq.shtml|link]] 
-| GFF   | Gene Feature Format | .gff | link | +| GFF   | Gene Feature Format | .gff | [[https://​genome.ucsc.edu/​FAQ/​FAQformat.html#​format3|link]] 
 | BED   | Browser Extensible Data | .bed | [[https://​genome.ucsc.edu/​FAQ/​FAQformat.html#​format1|link]] | | BED   | Browser Extensible Data | .bed | [[https://​genome.ucsc.edu/​FAQ/​FAQformat.html#​format1|link]] |
-| SAM   | Sequence Alignment Map | .sam | link |+| SAM   | Sequence Alignment Map | .sam | [[http://​www.htslib.org/​doc/​sam.html|link]] |
  
  
  
wiki/curtain_bin_vs_txt.1532730061.txt.gz · Last modified: 2018/07/27 16:21 by david